On 13/03/2012 12:54 AM, James Starlight wrote:
Dear Gromacs users!
I want to perform constrained MD simulation of my protein with
inclusion of some experimental restraints.
1) I found that genrest cpmmand could be usefull for the generation of
the distance restrictions wich I could use in my constrined simulation.
Also in manual I've found that command like
genrestr -f b2ar.gro -disre -index.ndx -o test.itp
... which should read "-n index.ndx". Please get in the habit of copying
and pasting actual command lines that you have observed to function like
you think they do :-). Then you won't mis-type something sometime that
will cause everyone to waste their time.
will produce some distance restricted matrix of the whole groups
presented in the index.ndx file.
So how I could select to contrain selected residues within selected
distance by means the index file? E.g I've manually point out 2
residues in index.ndx. I waant to preserve between that residues some
desired distance D wich I've obtaine from the experimental data. How I
could do it via genrestr and waht addition flags should I use for that
purpose ?
You need an index file that has a group or groups that do what you want.
Some details on the webpage. Since you know already the 2 atoms you care
about, you can make it in a text editor faster than writing this email
:-) Or indeed just constructing a [ distance_restraints ] section of the
[ moleculetype ] in consultation with the information in chapters 4 and
5 faster still.
2) Is there any way to apply gradually the desired dist.resrs during
MDrun to prevent some artifacts in my system wich would occur due to
the rapid application of the dis.res ( e.g in cases where the
conformation of the started structure and that wich I'd obtained fter
application of the restrains are slightly different)?
Only by choosing a gentle restraint at first and picking a time interval
at which to increase it.
Mark
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